The difference between American baseball and Japanese baseball is mostly in the stands. Well, it seems that the Japanese are fond of having dirt infields, whereas in the US they're invariably either grass or artificial turf.
Aside from that, judging from the college game that I went to, the Japanese have bands and cheerleaders at the games, and the cheerleaders are continuously leading cheers throughout the course of the game, almost to the point that you can't keep up with the action. Before the game the cheerleaders also performed, and there was some sort of ceremony where each school played its school song, and some guy wearing traditional Japanese garb yelled some stuff (I really don't know what that was about, and I couldn't make out anything he was saying).
In the US, there are never cheerleaders or bands at games. The only music you'll hear is the national anthem(s), and people are mostly quiet unless something exciting happens.
Again, since I've only been to one college game in Japan, so things may be different in the pro leagues (well, I'm sure they don't have a school song to play beforehand).